Publication in EndNote Format

%0 Journal Article
%A Paley, S. and Karp, P.D.
%T Evaluation of computational metabolic-pathway predictions for Helicobacter
pylori.
%B Bioinformatics
%P 715-24
%V 18
%D 2002
%X MOTIVATION: We seek to determine the accuracy of computational methods for predicting
metabolic pathways in sequenced genomes, and to understand the contributions
of both the prediction algorithms, and the reference pathway databases
used by those algorithms, to the prediction accuracy. RESULTS: The comparisons
we performed were as follows. (1) We compared two predictions of
the pathway complements of Helicobacter pylori that were computed by an
early version of our pathway-prediction algorithm: prediction A used the
EcoCyc E. coli pathway DB as the reference database (DB) for prediction,
and prediction B used the MetaCyc pathway DB (a superset of EcoCyc) as the reference
pathway DB. The MetaCyc-based prediction contained 75% more pathway
predictions, but we believe a significant number of those predictions
were false positives. (2) We compared two predictions of the pathway complement
of H. pylori that used MetaCyc as the reference pathway DB, but that
used different algorithms: the original PathoLogic algorithm, and
an enhanced version of the algorithm designed to eliminate false-positive pathway
predictions. The improved algorithm predicted 30\% fewer metabolic
pathways than the original algorithm; all of the eliminated pathways
are believed to be false-positive predictions. (3) We compared the 98 pathways
predicted by the enhanced algorithm with the results of a manual
analysis of the pathways of H. pylori. Results: 40 of the computationally
predicted pathways were consistent with the manual analysis, 13 pathways
are considered false-positive predictions, and four pathways had
partially overlapping topologies. Twenty-six predicted pathways were not mentioned
in the manual analysis; we believe these are correct predictions
by PathoLogic that were not found by the manual analysis. Five pathways
from the manual analysis were not found computationally. Agreement between the
computational and manual predictions was good overall, with the computational
analysis inferring many pathways that the manual analysis did not
identify. Ultimately the manual analysis is also partially speculative, and therefore
is not an absolute measure of correctness. The algorithm is designed
to err on the side of more false positives to bring more potential
pathways to the user’s attention. The resulting H. pylori pathway DB is
freely available at http://ecocyc.org:1555/HPY/organism-summary?object=HPY.
AVAILABILITY: The Pathway Tools software is freely available to academic
users, and is available to commercial users for a fee.
%N 5